Structure of PDB 4kvj Chain A Binding Site BS01

Receptor Information

>4kvj Chain A (length=611) Species: 4530 (Oryza sativa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GSVHPDLRDVFSKMSFFDKIGFLFIHAFDKRNLWHKVPVPIGLLYLNTRR
TLLEKYNLLAVGRSSHGALFDPKEFLYRTEDGKYNDPHNAEAGSQNTFFG
RNMEPVDQQDELMSPDPFVVATKLLARREYKDTGKQFNILAAAWIQFMVH
DWMDHMEDTGQIGITAPKEVANECPLKSFKFHPTKELPTNSDGIKIGHYN
IRTAWWDGSAVYGNNEERAEKLRTYVDGKLVIGDDGLLLHKENGVALSGD
IRNSWAGVSILQALFVKEHNAVCDAIKEEHPNLSDEELYRYAKLVTSAVI
AKVHTIDWTVELLKTKTMRAAMRANWYGLLGKKIKDTFGHIGGPILGGLV
GLKKPNNHGVPYSLTEEFTSVYRMHSLIPSTLKLRDPTGQPDANNSPPCL
EDIDIGEMIGLKGEEQLSKIGFEKQALSMGYQACGALELWNYPSFFRNLI
PQNLDGTNRSDRIDLAALEVYRDRERSVPRYNEFRRRLFLIPIKSWEDLT
SDKDAIETIRAIYGDDVEKLDLLVGLMAEKKIKGFAISETAFNIFILMAS
RRLEADRFFTSNFNEETYTKKGMQWVKTTEGLRDVINRHYPEITAKWMKS
SSAFSVWDADY

Ligand information

Ligand ID

HEM

InChI

InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;

InChIKey

KABFMIBPWCXCRK-RGGAHWMASA-L

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385	CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5\|6\|N2=C1C=c7n5c(=CC8=N\|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01	C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O

Formula

C34 H32 Fe N4 O4

Name

PROTOPORPHYRIN IX CONTAINING FE;
HEME

PDB chain

4kvj Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	4kvj Crystal structures of alpha-dioxygenase from Oryza sativa: Insights into substrate binding and activation by hydrogen peroxide.
Resolution	2.12 Å
Binding residue (original residue number in PDB)	I152 Q153 H162 N260 W262 T376 Y379 H382 I416 F453 L472 L475 R479 R483
Binding residue (residue number reindexed from 1)	I145 Q146 H155 N253 W255 T369 Y372 H375 I409 F446 L465 L468 R472 R476
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	Q153 H157 V378 Y379 H382 N550
Catalytic site (residue number reindexed from 1)	Q146 H150 V371 Y372 H375 N543
Enzyme Commision number	1.13.11.92: fatty acid alpha-dioxygenase.

Gene Ontology

	Molecular Function
GO:0004601	peroxidase activity
GO:0016491	oxidoreductase activity
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0020037	heme binding
GO:0046872	metal ion binding
GO:0051213	dioxygenase activity

	Biological Process
GO:0001561	fatty acid alpha-oxidation
GO:0006631	fatty acid metabolic process
GO:0006633	fatty acid biosynthetic process
GO:0006952	defense response
GO:0006979	response to oxidative stress
GO:0009627	systemic acquired resistance
GO:0009737	response to abscisic acid
GO:0009751	response to salicylic acid
GO:0031408	oxylipin biosynthetic process
GO:0034614	cellular response to reactive oxygen species
GO:0042742	defense response to bacterium
GO:0050832	defense response to fungus
GO:0071446	cellular response to salicylic acid stimulus
GO:0071732	cellular response to nitric oxide
GO:0098869	cellular oxidant detoxification
GO:1902609	(R)-2-hydroxy-alpha-linolenic acid biosynthetic process

	Cellular Component
GO:0012511	monolayer-surrounded lipid storage body

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Cellular Component

External links

PDB	RCSB:4kvj, PDBe:4kvj, PDBj:4kvj
PDBsum	4kvj
PubMed	23934749
UniProt	Q2QRV3\|PIOX_ORYSJ Alpha-dioxygenase PIOX (Gene Name=PIOX)

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